Searching journal content for articles similar to Galagan et al. 12 (4): 532.

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  1. Method: Control of fluxes in metabolic networks
    • Georg Basler,
    • Zoran Nikoloski,
    • Abdelhalim Larhlimi,
    • Albert-László Barabási,
    • and Yang-Yu Liu
    Genome Res. July 2016 26: 956-968; Published in Advance May 19, 2016, doi:10.1101/gr.202648.115
    ...be controlled Table 1. Metabolic networks analyzed in this study C Network n d Description Reference 1 M acetivorans iMB745 628 18.3 Genome-scale metabolic network of Methanosarcina acetivorans (Satish Kumar et al. 2011) M barkeri iAF692 537 16.7 Genome-scale metabolic network of Methanosarcina barkeri (Feist...
  2. LETTER: The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota
    • Tomoyuki Kosaka,
    • Souichiro Kato,
    • Takefumi Shimoyama,
    • Shunichi Ishii,
    • Takashi Abe,
    • and Kazuya Watanabe
    Genome Res. March 2008 18: 442-448; Published in Advance January 24, 2008, doi:10.1101/gr.7136508
    ...The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota Tomoyuki Kosaka 1 , 2 , 5 , Souichiro Kato 1 , Takefumi Shimoyama 1 , Shunichi Ishii 1 , 5 , Takashi Abe 3 , and Kazuya...
  3. ARTICLE: Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
    • Neil F.W. Saunders,
    • Torsten Thomas,
    • Paul M.G. Curmi,
    • John S. Mattick,
    • Elizabeth Kuczek,
    • Rob Slade,
    • John Davis,
    • Peter D. Franzmann,
    • David Boone,
    • Karl Rusterholtz,
    • Robert Feldman,
    • Chris Gates,
    • Shellie Bench,
    • Kevin Sowers,
    • Kristen Kadner,
    • Andrea Aerts,
    • Paramvir Dehal,
    • Chris Detter,
    • Tijana Glavina,
    • Susan Lucas,
    • Paul Richardson,
    • Frank Larimer,
    • Loren Hauser,
    • Miriam Land,
    • and Ricardo Cavicchioli
    Genome Res. July 2003 13: 1580-1588; Published in Advance June 12, 2003, doi:10.1101/gr.1180903
    ..., P., FitzHugh, W., Calvo, S., Engels, R., Smirnov, S., Atnoor, D., et al. 2002 . The of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12 : 532 -542. ↵ Galtier, N. and Lobry, J.R. 1997 . Relationships between genomic G+C content, RNA secondary structures...
  4. ARTICLE: Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
    • Minglei Wang,
    • Liudmila S. Yafremava,
    • Derek Caetano-Anollés,
    • Jay E. Mittenthal,
    • and Gustavo Caetano-Anollés
    Genome Res. November 2007 17: 1572-1585; Published in Advance October 1, 2007, doi:10.1101/gr.6454307
    ...these architectural chronologies revealed patterns of discovery of biological function. Most importantly, the analysis identified an early and extensive differential loss of architectures occurring primarily in Archaea that segregates the archaeal lineage from the ancient community of organisms and establishes...
  5. COMMENTARY: Community annotation: Procedures, protocols, and supporting tools
    • Christine G. Elsik,
    • Kim C. Worley,
    • Lan Zhang,
    • Natalia V. Milshina,
    • Huaiyang Jiang,
    • Justin T. Reese,
    • Kevin L. Childs,
    • Anand Venkatraman,
    • C. Michael Dickens,
    • George M. Weinstock,
    • and Richard A. Gibbs
    Genome Res. November 2006 16: 1329-1333; Published in Advance October 25, 2006, doi:10.1101/gr.5580606
    .... , Smirnov, S. , Atnoor, D. , et al. ( 2002 ) The of M. acetivorans reveals extensive metabolic and physiological diversity . Genome Res. 12 : 532 – 542 . ↵ Glasner, J.D. , Liss, P. , Plunkett, G. , III , Darling, A. , Prasad, T. , Rusch, M. , Byrnes, A. , Gilson, M. , Biehl, B. , Blattner, F.R. , et al...
    OPEN ACCESS ARTICLE
  6. Methods: Identification of genomic features using microsyntenies of domains: Domain teams
    • Sophie Pasek,
    • Anne Bergeron,
    • Jean-Loup Risler,
    • Alexandra Louis,
    • Emmanuelle Ollivier,
    • and Mathieu Raffinot
    Genome Res. June 2005 15: 867-874; Published in Advance May 17, 2005, doi:10.1101/gr.3638405
    ...., Fischer, C., Ozouf-Costaz, C., Bernot, A., et al. 2004 . Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431 : 946 -957. ↵ Kadner, R.J. 1996 . Cytoplasmic membrane. In Escherichia coli and Salmonella typhimurium, cellular and molecular...
  7. LETTER: Functional insights from the distribution and role of homopeptide repeat-containing proteins
    • Noel G. Faux,
    • Stephen P. Bottomley,
    • Arthur M. Lesk,
    • James A. Irving,
    • John R. Morrison,
    • Maria Garcia de la Banda,
    • and James C. Whisstock
    Genome Res. April 2005 15: 537-551; doi:10.1101/gr.3096505
    ...RCPs were annotated using BLASTp searches and Gene Ontology. These data reveal that the majority of RCPs are involved in processes that require the assembly of large, multiprotein complexes, such as transcription and signaling. Footnotes [Supplemental material is available online at www.genome...
  8. LETTER: Prokaryotic phylogenies inferred from protein structural domains
    • Eric J. Deeds,
    • Hooman Hennessey,
    • and Eugene I. Shakhnovich
    Genome Res. March 2005 15: 393-402; doi:10.1101/gr.3033805
    ...structural domains within fully sequenced prokaryotic genomes. The evolution of the structural domains we use has been studied extensively, allowing us to base our phylogenetic methods on testable theoretical models of structural evolution. We find that the methods that produce reasonable phylogenetic...
  9. ARTICLE: The Complete Genome and Proteome of Mycoplasma mobile
    • Jacob D. Jaffe,
    • Nicole Stange-Thomann,
    • Cherylyn Smith,
    • David DeCaprio,
    • Sheila Fisher,
    • Jonathan Butler,
    • Sarah Calvo,
    • Tim Elkins,
    • Michael G. FitzGerald,
    • Nabil Hafez,
    • Chinnappa D. Kodira,
    • John Major,
    • Shunguang Wang,
    • Jane Wilkinson,
    • Robert Nicol,
    • Chad Nusbaum,
    • Bruce Birren,
    • Howard C. Berg,
    • and George M. Church
    Genome Res. August 2004 14: 1447-1461; doi:10.1101/gr.2674004
    ...Required Core Set). Using these methods, we have suggested several genes that might be involved in motility in the mycoplasmas. We hope that these predictions can be tested experimentally in the future. To that end, genomic sequencing has now revealed several DNA restriction/modification systems that might...
  10. ARTICLE: Comparative Analysis of Protein Domain Organization
    • Yuzhen Ye and
    • Adam Godzik
    Genome Res. March 2004 14: 343-353; doi:10.1101/gr.1610504
    ...and compare >50 bacterial, archaeal, and eukaryotic genomes. Examples and overviews presented here include the analysis of the modularity of domain graphs and the functional study of domains based on the graph topology. We also report on the results of comparing domain graphs of two organisms, Pyrococcus...
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